Design of a bistable switch to control cellular uptake

Abstract

Bistable switches are widely used in synthetic biology to trigger cellular functions in response to environmental signals. All bistable switches developed so far, however, control the expression of target genes without access to other layers of the cellular machinery. Here, we propose a bistable switch to control the rate at which cells take up a metabolite from the environment. An uptake switch provides a new interface to command metabolic activity from the extracellular space and has great potential as a building block in more complex circuits that coordinate pathway activity across cell cultures, allocate metabolic tasks among different strains or require cell-to-cell communication with metabolic signals. Inspired by uptake systems found in nature, we propose to couple metabolite import and utilization with a genetic circuit under feedback regulation. Using mathematical models and analysis, we determined the circuit architectures that produce bistability and obtained their design space for bistability in terms of experimentally tuneable parameters. We found an activation-repression architecture to be the most robust switch because it displays bistability for the largest range of design parameters and requires little fine-tuning of the promoters' response curves. Our analytic results are based on on -off approximations of promoter activity and are in excellent qualitative agreement with simulations of more realistic models. With further analysis and simulation, we established conditions to maximize the parameter design space and to produce bimodal phenotypes via hysteresis and cell-to-cell variability. Our results highlight how mathematical analysis can drive the discovery of new circuits for synthetic biology, as the proposed circuit has all the hallmarks of a toggle switch and stands as a promising design to control metabolic phenotypes across cell cultures.

Stochastic modelling reveals mechanisms of metabolic heterogeneity

“…The other two regimes, however, correspond to alternative routes of noise-induced bimodality that cannot be explained using deterministic models [41][42][43] . Regime (2) is a highly stochastic regime dominated by the slow stochastic switching of the promoter, which drives and entrains the metabolic response.…”

Dynamics of complex feedback architectures in metabolic pathways

“…Regulatory motifs in metabolic systems include architectures with various combinations of feedback and feedforward loops, whose signs and interactions determine the overall pathway dynamics. A fundamental design problem is the characterization of control architectures that achieve a prescribed system response [33,23]. However, there are no general stability analysis methods that can deal with the type of nonlinearities and connectivity of metabolic systems.…”

Dynamic metabolic control: towards precision engineering of metabolism

“…A particularly promising use for modelling is the exploration of circuit architectures. Models have been used to search for architectures that efficiently trade-off production flux against toxicity effects by metabolic intermediates [61], to explore circuit architectures that function robustly in the face of environmental or genetic perturbations [25], or to discover new useful architectures, such as a bistable metabolic switch that filters out fluctuations in nutrient availability [43].…”

“…Challenges for designing dynamic control circuits at various levels. These challenges include how to tune parts to obtain desired dose-response functions, when control is actuated by riboswitches [6,52] or transcription factors [40,63]; how regulatory architectures affect dynamics [17,46,61] and robustness [43], as learned from models of natural control systems; how to balance limited resources between growth and production, studied theoretically…”